R We There Yet? Visualizing MCMC Convergence in Phylogenetics
analyze.rwty, the main interface for rwty analyses and plots.
Function for checking suitability of chains for rwty analyses, auto-ge...
Returns clade names and frequencies
Function for merging p tables for multiple MCMC chains
Cumulative means of clade split frequencies.
Calculate sampling interval based on exponential semivariogram model.
Load all matching files from a directory into a list of rwty.chain obj...
Custom functions to load tree lists so that rwty can do basic processi...
Plot the Change in Split Frequencies (CSF) in sliding windows over the...
Plot the Chaing in Split Frequencies (CSF) in sliding windows over the...
Plotting all parameters
Plot the Standard Deviation of Split Frequencies over the course of an...
Make autocorrelation plots of tree topologies from MCMC analyses
Plotting parameters against each other
Plotting parameters
Plot the pseudo ESS of tree topologies from MCMC chains.
Plots a matrix of split frequency comparisons between multiple MCMC ch...
Plot cumulative split frequencies over the course of an MCMC
Plot split frequencies in sliding windows over the course of an MCMC
Plotting parameters
Plot chains in treespace.
Rename clades for easy recall
Function for printing rwty.chain objects
Sliding window measurements of clade split frequencies.
Calculate the approximate Effective Sample Size (ESS) of tree topologi...
Calculate data for autocorrelation plots of tree topologies from MCMC ...
Calculate the pseudo Effective Sample Size (ESS) of tree topologies
Tree distance matrix calculation
MDS scaling of treespace for a single tree list.
Implements various tests, visualizations, and metrics for diagnosing convergence of MCMC chains in phylogenetics. It implements and automates many of the functions of the AWTY package in the R environment.